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Related Experiment Video

Updated: Dec 29, 2025

Testing the Role of Multicopy Plasmids in the Evolution of Antibiotic Resistance

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Published on: May 2, 2018

Bacterial Origin and Reductive Evolution of the CPR Group.

Rijja Hussain Bokhari¹, Nooreen Amirjan¹, Hyeonsoo Jeong²

¹Department of Biosciences, COMSATS University Islamabad, Pakistan.

Genome Biology and Evolution

|February 8, 2020

Summary

Candidate Phyla Radiation (CPR) organisms are deep-branching bacteria. Our study reveals they evolved via early metabolic gene loss, similar to Archaea, impacting bacterial evolution and superkingdom relationships.

Keywords:

candidate phyla radiation phylogenetics protein structure reductive evolution tree of life

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Testing the Role of Multicopy Plasmids in the Evolution of Antibiotic Resistance

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CAPRRESI: Chimera Assembly by Plasmid Recovery and Restriction Enzyme Site Insertion

CAPRRESI: Chimera Assembly by Plasmid Recovery and Restriction Enzyme Site Insertion

Published on: June 25, 2017

Area of Science:

Microbiology
Evolutionary Biology
Bioinformatics

Background:

Candidate Phyla Radiation (CPR) represents a unique bacterial lineage with small genomes and lost metabolic functions.
CPR's deep branching position and distinct features raise questions about their evolutionary origins and relationships with other life domains.

Purpose of the Study:

To investigate the evolutionary origin and relationships of CPR organisms.
To resolve CPR's phylogenetic position using protein domain superfamilies.

Main Methods:

Comparative and phylogenomic analysis using protein domain superfamilies from protein structure databases.
Phylogenetic tree construction incorporating CPR, non-CPR bacteria, Archaea, Eukarya, and viruses.
Analysis of protein superfamily gains and losses, particularly metabolic ones.

Main Results:

CPR organisms are confirmed as deep-branching bacteria, sharing most superfamilies with non-CPR bacteria.
CPR contributed novel superfamilies to bacteria and possesses core superfamilies linked to cell-cell interaction and symbiosis.
CPR and Archaea show significant common losses in metabolic superfamilies, distinguishing them from non-CPR bacteria.

Conclusions:

CPR likely evolved through early loss of metabolic functions, adopting an Archaea-like evolutionary strategy.
Metabolic and informational superfamilies yield contrasting phylogenetic views, contributing to ongoing debates on superkingdom evolutionary relationships.